Originally named the Red Eagles Brigades the Brigades were renamed in 2001 after Abu Ali Mustafa, the PFLP's leader who was killed by Israel in August 2001. They have been active with attacks on both military and civilian Israeli targets during the al-Aqsa Intifada.

On the 16 July 2007, Palestinian president Mahmoud Abbas requested of all Palestinian resistance groups to relinquish their weapons to the Palestinian Authority. Although several members of Fatah's armed wing Al-Aqsa Martyrs' Brigades complied, the Abu Ali Mustafa brigades rejected this, stating that they will not cease their resistance until the Israelis unoccupy all parts of the West Bank and the Gaza Strip.

The 17 October 2001 assassination of right-wing Israeli politician and Israeli Minister for Tourism Rehavam Zeevi, the only Israeli politician to have been assassinated in the al-Aqsa intifada.

A suicide bombing in a pizzeria in Karnei Shomron in the West Bank, on 16 February 2002, killing three Israelis.

A suicide bombing in Ariel on 7 March 2002, which left wounded but no fatalities.

A suicide bombing in a Netanya market in Israel, on 19 May 2002, killing three Israelis. This attack was also claimed by Hamas, but the Abu Ali Mustafa Brigades have identified the perpetrator on their website as one of their members.[4]